HAL's MD package

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Latest stable release: 0.2.0

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Introduction

HAL’s MD package (HALMD) is a high-precision molecular dynamics package for the large-scale simulation of simple and complex liquids. HALMD supports acceleration through CUDA-enabled graphics processors. HALMD lays emphasis on long-time numerical stability by using double-single precision arithmetic for numerically crucial parts of the MD integration step. HALMD is freely available and licensed under the GPL.

HAL’s MD package is maintained and developed by Felix Höfling and was initially written together with Peter Colberg.

Note

A description of the implementation, performance tests, numerical stability tests and an application to the glass transition of the Kob-Andersen mixture is found in the article by Peter H. Colberg and Felix Höfling, Highly accelerated simulations of glassy dynamics using GPUs: Caveats on limited floating-point precision, Comp. Phys. Comm. 182, 1120 (2011) [arXiv:0912.3824].

The name HAL’s MD package was chosen in honour of the machine HAL at the Arnold Sommerfeld Center for Theoretical Physics of the Ludwigs-Maximilians-Universität München. HAL has been the project’s first GPGPU machine, equipped initially with two NVIDIA GeForce 8800 Ultra. HAL survived a critical air condition failure and to this day houses two NVIDIA GeForce GTX 280.

Features

HAL’s MD package features

  • GPU acceleration by up to a factor of 80 (with GeForce GTX 280),
  • double-single arithmetic for excellent numerical long-time stability,
  • potential smoothing for optimal energy conservation,
  • online evaluation of various dynamic correlation functions,
  • simulations at constant energy in the NVE ensemble,
  • Andersen thermostat for NVT simulations.

Physics applications

HAL’s MD package is designed to study

  • the dynamics of simple liquids and binary mixtures,
  • particles interacting via attractive or purely repulsive potentials (truncated and shifted Lennard-Jones potentials),
  • both two- and three-dimensional systems.

Technical features

HAL’s MD package employs

  • simulation parameters passed via command line options, INI-style configuration files and HDF5 output files,
  • compressed and structured output of trajectories, thermodynamic variables and correlation functions in HDF5 format,
  • a modular design with various backends loaded as dynamic libraries or separate executables,
  • easily extensible template-based C++ code.